Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family

BMC Molecular Biology

Volumn 10, Issue , 2009, Pages

  Zylicz Stachula, Agnieszka ^a   Bujnicki, Janusz M ^b,c   Skowron, Piotr M ^a  

^a UNIVERSITY OF GDA SK   (Poland)

^b INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

^c ADAM MICKIEWICZ UNIVERSITY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; DIVALENT CATION; METHYLTRANSFERASE; RESTRICTION ENDONUCLEASE; S ADENOSYLHOMOCYSTEINE; S ADENOSYLMETHIONINE; TAQ POLYMERASE; TAQII ENZYME; TSPGWI ENZYME; UNCLASSIFIED DRUG; DNA METHYLTRANSFERASE;

ALLOSTERISM; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CONTROLLED STUDY; DNA SEQUENCE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME MODIFICATION; ENZYME SUBUNIT; ENZYMOLOGY; MOLECULAR CLONING; MUTAGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; THERMUS; WILD TYPE; CHEMISTRY; GENETICS; METABOLISM; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; SITE DIRECTED MUTAGENESIS;

THERMUS SP.;

AMINO ACID SEQUENCE; CLONING, MOLECULAR; DNA MODIFICATION METHYLASES; DNA RESTRICTION ENZYMES; DNA RESTRICTION-MODIFICATION ENZYMES; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; THERMUS;

EID: 67649421630     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-10-52     Document Type: Article

References (50)

1. Roberts RJ Restriction enzymes and their isoschizomers Nucleic Acids Res 1990, 18(Suppl):2331-2365. 331877 2159140
2. Roberts RJ Belfort M Bestor T Bhagwat AS Bickle TA Bitinaite J Blumenthal RM Degtyarev SK Dryden DT Dybvig K Firman K Gromova ES Gumport RI Halford SE Hattman S Heitman J Hornby DP Janulaitis A Jeltsch A Josephsen J Kiss A Klaenhammer TR Kobayashi I Kong H Kruger DH Lacks S Marinus MG Miyahara M Morgan RD Murray NE Nagaraja V Piekarowicz A Pingoud A Raleigh E Rao DN Reich N Repin VE Selker EU Shaw PC Stein DC Stoddard BL Szybalski W Trautner TA Van Etten JL Vitor JM Wilson GG Xu SY A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes Nucleic Acids Res 2003, 31:1805-1812. 152790 12654995 10.1093/nar/gkg274
3. Dryden DT Murray NE Rao DN Nucleoside triphosphate-dependent restriction enzymes Nucleic Acids Res 2001, 29(18):3728-3741. 55918 11557806 10.1093/ nar/29.18.3728
4. Pingoud A Fuxreiter M Pingoud V Wende W Type II restriction endonucleases: Structure and mechanism Cell Mol Life Sci 2005, 62:685-707. 10.1007/s00018-004-4513-1 15770420
5. Roberts RJ Vincze T Posfai J Macelis D REBASE-enzymes and genes for DNA restriction and modification Nucleic Acids Res 2007, 33:D269-D270. 10.1093/nar/gkl891
6. Ishikawa K Watanabe M Kuroita T Uchiyama I Bujnicki JM Kawakami B Tanokura M Kobayashi I Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5′-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi Nucleic Acids Res 2005, 33:e112. 1178009 16040595 10.1093/nar/gni113
7. Pingoud V Conzelmann C Kinzebach S Sudina A Metelev V Kubareva E Bujnicki JM Lurz R Luder G Xu SY Pingoud A PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: Structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes J Mol Biol 2003, 329:913-929. 10.1016/S0022-2836(03)00523-0 12798682
8. Morgan R Xiao J Xu S Characterization of an extremely thermostable restriction enzyme, PspGI, from a Pyrococcus strain and cloning of the PspGI restriction-modification system in Escherichia coli Appl Environ Microbiol 1998, 64:3669-3673. 106503 9758783
9. Skowron PM Majewski J Zylicz-Stachula A Rutkowska SM Jaworowska I Harasimowicz-Slowinska RI A new Thermus sp. class-IIS enzyme sub-family: isolation of a 'twin' endonuclease TspDTI with a novel specificity 5′-ATGAA(N(11/9))-3′, related to TspGWI, TaqII and Tth111II Nucleic Acids Res 2003, 31:e74. 167652 12853651 10.1093/nar/gng074
10. Zylicz-Stachula A Harasimowicz-Slowinska RI Sobolewski I Skowron PM TspGWI, a thermophilic class-IIS restriction endonuclease from Thermus sp., recognises novel asymmetric sequence 5′-ACGGA(N11/9)-3′ Nucleic Acids Res 2002, 30:e33. 101857 11917039 10.1093/nar/30.7.e33
11. Vitkute J Maneliene Z Janulaitis A Two new thermostable type II restriction endonucleases from Thermus aquaticus: TatI and TauI, which recognise the novel nucleotide sequences 5′-W (downward arrow)GTACW-3′ and 5′-GCSG (downward arrow)C-3′ respectively FEMS Microbiol Lett 2001, 204:253-257. 11731131
12. Cao W Lu J Welch SG Williams RA Barany F Cloning and thermostability of TaqI endonuclease isoschizomers from Thermus species SM32 and Thermus filiformis Tok6A1 Biochem J 1998, 333:425-431. 1219601 9657984
13. Cao W Lu J Barany F Nucleotide sequences and gene organization of TaqI endonuclease isoschizomers from Thermus sp. SM32 and Thermus filiformis Tok6A1 Gene 1997, 197:205-214. 10.1016/S0378-1119(97)00264-3 9332368
14. Barker D Hoff M Oliphant A White R A second type II restriction endonuclease from Thermus aquaticus with an unusual sequence specificity Nucleic Acids Res 1984, 12:5567-5581. 320015 6087291 10.1093/nar/ 12.14.5567
15. Shinomiya T Kobayashi M Sato S A second site specific endonuclease from Thermus thermophilus 111, Tth111II Nucleic Acids Res 1980, 8:3275-3285. 324152 6255411 10.1093/nar/8.15.3275
16. Janulaitis A Petrusyte M Maneliene Z Klimasauskas S Butkus V Purification and properties of the Eco57I restriction endonuclease and methylase-prototypes of a new class (type IV) Nucleic Acids Res 1992, 20:6043-6049. 334471 1334260 10.1093/nar/20.22.6043
17. Janulaitis A Vaisvila R Timinskas A Klimasauskas S Butkus V Cloning and sequence analysis of the genes coding for Eco57I type IV restriction-modification enzymes Nucleic Acids Res 1992, 20:6051-6056. 334472 1334261 10.1093/nar/20.22.6051
18. Piekarowicz A Golaszewska M Sunday AO Siwinska M Stein DC The HaeIV restriction modification system of Haemophilus aegyptius is encoded by a single polypeptide J Mol Biol 1999, 293:1055-1065. 10.1006/ jmbi.1999.3198 10547285
19. Cesnaviciene E Petrusyte M Kazlauskiene R Maneliene Z Timinskas A Lubys A Janulaitis A Characterization of AloI, a restriction-modification system of a new type J Mol Biol 2001, 314:205-216. 10.1006/ jmbi.2001.5049 11718555
20. Jurenaite-Urbanaviciene S Kazlauskiene R Urbelyte V Maneliene Z Petrusyte M Lubys A Janulaitis A Characterization of BseMII, a new type IV restriction-modification system, which recognises the pentanucleotide sequence 5′-CTCAG(N)(10/8) Nucleic Acids Res 2001, 29:895-903. 29615 11160921 10.1093/nar/29.4.895
21. Barker D Hoff M Oliphant A White R A second type II restriction endonuclease from Thermus aquaticus with an unusual sequence specificity Nucleic Acids Res 1984, 12(14):5567-5581. 320015 6087291 10.1093/nar/ 12.14.5567
22. Kosinski J Feder M Bujnicki JM The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function BMC Bioinformatics 2005, 6:172. 1189080 16011798 10.1186/1471-2105-6-172
23. Kurowski MA Bujnicki JM GeneSilico protein structure prediction meta-server Nucleic Acids Res 2003, 31:3305-3307. 168964 12824313 10.1093/nar/gkg557
24. Kennaway CK Obarska-Kosinska A White JH Tuszynska I Cooper LP Bujnicki JM Trinick J Dryden DT The structure of M. EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein Nucleic Acids Res 2008, 37(3):762-770. doi:10.1093/nar/gkn988. 2647291 19074193 10.1093/nar/gkn988
25. Obarska-Kosinska A Taylor JE Callow P Orlowski J Bujnicki JM Kneale GG HsdR subunit of the Type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling J Mol Biol 2008, 376:438-452. 10.1016/j.jmb.2007.11.024 18164032
26. Orlowski J Bujnicki JM Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses Nucleic Acids Res 2008, 36(11):3552-3569. 2441816 18456708 10.1093/nar/gkn175
27. Davies GP Martin I Sturrock SS Cronshaw A Murray NE Dryden DT On the structure and operation of type I DNA restriction enzymes J Mol Biol 1999, 290:565-579. 10.1006/jmbi.1999.2908 10390354
28. Nakonieczna J Kaczorowski T Obarska-Kosinska A Bujnicki JM Functional analysis of the MmeI restriction-modification enzyme from a methanol utilizer Methylophilus methylotrophus: A subtype IIC enzyme related to Type I enzymes Appl Environ Microbiol 2009, 75(1):212-223. doi:10.1128/ AEM.01322-08. 10.1128/AEM.01322-08 18997032
29. Jurenaite S Kazlauskiene R Urbelyte V Maneliene Z Petrusyte M Lubys A Janulaitis A Characterization of BseMII, a new type IV restriction-modification system, which recognises the pentanucleotide sequence 5′ CTCAG (N)10/8 Nucleic Acids Res 2001, 29:895-903. 29615 11160921 10.1093/nar/29.4.895
30. Kong H Roemer SE Waite-Rees PA Benner JS Wilson GG Nwankwo DO Characterization of BcgI, a new kind of restriction-modification system J Biol Chem 1994, 269:683-690. 8276869
31. Kong H Morgan RD Maunus RE Schildkraut I A unique restriction endonuclease, BcgI, from Bacillus coagulans Nucleic Acids Res 1993, 21:987-991. 309233 8451198 10.1093/nar/21.4.987
32. Degtyarev SK Rechkunova NI Zernov YP Dedkov VS Chizikov VE Van Calligan M Bsp24I, a new unusual restriction endonuclease Gene 1993, 131:93-95. 10.1016/0378-1119(93)90674-R 8396549
33. Sears LE Zhou B Aliotta JM Morgan RD Kong H BaeI, another unusual BcgI-like restriction endonuclease Nucleic Acids Res 1996, 24:3590-3592. 146138 8836187 10.1093/nar/24.18.3590
34. Vitkute J Maneliene Z Petrusyte M Janulaitis A BplI, a new BcgI-like restriction endonuclease, which recognises a symmetric sequence Nucleic Acids Res 1997, 25:4444-4446. 147065 9358150 10.1093/nar/25.22.4444
35. Meisel A Bickle TA Kruger DH Schroeder C Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage Nature 1992, 355:467-469. 10.1038/355467a0 1734285
36. Kingston IJ Gormley NA Halford S DNA supercoiling enables the type IIS restriction endonuclease BspMI to recognise the relative orientation of two DNA sequences Nucleic Acids Res 2003, 31:5221-5228. 203326 12954757 10.1093/nar/gkg743
37. Embleton ML Siksnys V Halford SE DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites J Mol Biol 2001, 311:503-514. 10.1006/jmbi.2001.4892 11493004
38. Bath AJ Milsom SE Gormley NA Halford SE Many type IIS restriction endonucleases interact with two recognition sites before cleaving DNA J Biol Chem 2002, 277:4024-4033. 10.1074/jbc.M108441200 11729187
39. Sambrook J Fitsch EF Maniatis T Molecular Cloning: A Laboratory Manual Cold Spring Harbor Press, Cold Spring Harbor, NY 1989.
40. Laemmli UK Cleavage of structural proteins during the assembly of the head of bacteriophage T4 Nature 1970, 227:680-685. 10.1038/227680a0 5432063
41. Chang AC Cohen SN Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid J Bacteriol 1978, 134:1141-1156. 222365 149110
42. Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997, 25:3389-3402. 146917 9254694 10.1093/ nar/25.17.3389
43. Edgar RC MUSCLE: Multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res 2004, 32:1792-1797. 390337 15034147 10.1093/ nar/gkh340
44. Kosinski J Kubareva E Bujnicki JM A model of restriction endonuclease MvaI in complex with DNA: A template for interpretation of experimental data and a guide for specificity engineering Proteins 2007, 68(1):324-36. 10.1002/prot.21460 17407166
45. Orlowski J Boniecki M Bujnicki JM I-Ssp6803I: The first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition Bioinformatics 2007, 23(5):527-30. 10.1093/ bioinformatics/btm007 17242028
46. Feder M Bujnicki JM Identification of a new family of putative PD-(D/ E)XK nucleases with unusual phylogenomic distribution and a new type of the active site BMC Genomics 2005, 6(1):21. 551604 15720711 10.1186/ 1471-2164-6-21
47. Lundstrom J Rychlewski L Bujnicki J Elofsson A Pcons: A neural-network-based consensus predictor that improves fold recognition Protein Sci 2001, 10:2354-2362. 2374055 11604541 10.1110/ps.08501
48. Kosinski J Cymerman IA Feder M Kurowski MA Sasin JM Bujnicki JM A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation Proteins 2003, 53(Suppl 6):369-379. 10.1002/prot.10545 14579325
49. Kosinski J Gajda MJ Cymerman IA Kurowski MA Pawlowski M Boniecki M Obarska A Papaj G Sroczynska-Obuchowicz P Tkaczuk KL Sniezynska P Sasin JM Augustyn A Bujnicki JM Feder M FRankenstein becomes a cyborg: The automatic recombination and realignment of fold recognition models in CASP6 Proteins 2005, 61(Suppl 7):106-113. 10.1002/prot.20726 16187351
50. Pawlowski M Gajda MJ Matlak R Bujnicki JM MetaMQAP: A meta-server for the quality assessment of protein models BMC Bioinformatics 2008, 9:403. 2573893 18823532 10.1186/1471-2105-9-403